onh_rnfl_thickness

src/MATLAB/+RSF/getImf.m

@@ -6,10 +6,10 @@ function imf = getImf(pData,radii)
 % radii = {[0.5,8,8]}; % plate
 
 % 
-% NGPU = HIP.Cuda.DeviceCount;
+NGPU = HIP.Cuda.DeviceCount;
 % p = ljsStartParallel(8*NGPU);
 
-N_CUDA_PROCS = 48;
+N_CUDA_PROCS = 16 * NGPU;
 startTarget = 1;
 imf = {};
 im1 = Composite();

src/MATLAB/clusterExamples/goLR.m

 tic
-ROOT = '/g/leverjs/Schuman_OCT/OCT/qualified';
+ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
 
 PID = 'P10010';
+% PID = 'P10125'
 flist = dir(fullfile(ROOT,['/' PID '*.LEVER']));
 mx = regexp({flist.name},'P(?<PID>\d+)_(?<scanType>.+)_(?<date>\d+-\d+-\d+)_(?<time>\d+-\d+-\d+)_(?<eye>\w\w)_(?<scanID>.+?)_.*.LEVER','names');
 tblMeta = struct2table(vertcat(mx{:}));
@@ -15,10 +16,10 @@ tblMeta = tblMeta(contains(tblMeta.scanType,'Optic'),:);
 
 p = ljsStartParallel(96);
 
-% radii = {[0.5,8,8],[5,5,5],[0,0,0]}; % plate,blob
+radii = {[0.5,8,8],[5,5,5],[0,0,0]}; % plate,blob
 % radii = {[0.5,8,8]}; % plate
 
-radii = {[3]} % dark tubes
+% radii = {[3]} % dark tubes
 imf = RSF.getImf(tblMeta,radii);
 d = [];
 parfor i = 1:length(imf)

src/MATLAB/importMetadata/readme.txt

+Hi Andy,
+
+Sorry for the messy spreads. But yes, those would be the files which contain the MD used in classification (column R).
+And yes the Project IDs should be associated with the image files.
+This data probably needed some tidying up before being shared but if you would still like to work on it its important to make sure that we use tests with
+•	threshold of  Visual Field 24-2 Test Pattern (column I)
+•	have a qualification_status of yes (column CE)
+•	have < 33% average false_positive_p, false_negative_p, fixation_loss_c_p (columns F,G,H) 
+
+In regards to multiple MDs on the same visit, besides the rows that are outright duplicates, please select the tests which have the lower total reliability errors (columns F,G,H).
+
+I hope that clarifies some of the issues, in the meantime I will work on resending a cleaner dataset!
+
+Best,
+Ronald

src/MATLAB/ncdVSvfmd/goKernelCorr.m

+SAVE_FOLDER = './results';
+if ~exist("SAVE_FOLDER",'dir')
+    mkdir('SAVE_FOLDER');
+end
 datetime
 kernelCorrStart = tic();
 eye = 'OD';
-ROOT = '/g/leverjs/Schuman_OCT/OCT/qualified';
+ROOT = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
 % scanType = 'Macular Cube 200x200';
 scanType = 'Optic Disc Cube 200x200';
 
@@ -12,11 +16,15 @@ tblMeta = getMetaOCT(ROOT,eye,scanType);
 
 load('../qualify/onh_rnfl_thickness.mat');
 
-radii = {[0.5,8,8],[5,5,5],[4]}; % plate,blob
-% radii = {[0.5,8,8]}; % plate
+% radii = {[0.5,8,8],[5,5,5],[8]}; % plate,blob
+% radii = {[0.5,8,8],[5,5,5],[0]}; % plate,blob
+radii = {[0.5,8,8]}; % plate
 
 
 [rho2,tblVelo, pData, dxx]  = kernelCorr(radii,tblVFMD,tblMeta,tblRNFL);
 
 
 [rmse1,~] = regnetCorr(tblVelo);median(rmse1)
+
+saveFile = fullfile(SAVE_FOLDER,['qualYes_ncdVSvfmd_' jsonencode(radii) '.mat']);
+save(saveFile)

src/MATLAB/ncdVSvfmd/regnetCorr.m

@@ -7,7 +7,7 @@ function [err,mdlX] = regnetCorr(tblVelo)
 % X = [tblVelo.ncd,tblVelo.md];
 t2 = tblVelo(tblVelo.dmd~=0,:);
 
-X1 = [t2.ncd];
+X1 = [t2.ncd,t2.deltaRNFL];
 X2 = [t2.ncd,t2.md];
 T = t2.dmd;
 % T = t2.deltaRNFL;
@@ -27,8 +27,11 @@ for i = 1:length(xTarget)
     mdlX{i} = mdl;
     pred = mdl.predict(xTarget(i,:));
     err(i) = abs(T(i) - pred);
-    [i,median(err)]
+    fprintf(1,'%d,%0.2f, ',i,median(err));
+    drawnow;    
+    if mod(i,10) == 0,fprintf(1,'\n');end
 end
+fprintf(1,'\n'); 
 % mean(err)
 4;
 

src/MATLAB/qualify/goQualify.m

 ROOT = '/g/leverjs/Schuman_OCT/OCT/combined';
-target = '/g/leverjs/Schuman_OCT/OCT/qualified';
+target = '/g/leverjs/Schuman_OCT/OCT/qualifiedYes';
 if ~exist(target,'dir')
     mkdir(target);
 end
-% flist = dir(fullfile(ROOT,'**/*.LEVER'));
-% qONH = readtable('nyu onh matched.xlsx');
-% qMacula = readtable('nyu mac matched.xlsx');
-% [~,fONH,~] = fileparts(qONH.file_name);
-% [~,fMacula,~] = fileparts(qMacula.file_name);
+flist = dir(fullfile(ROOT,'**/*.LEVER'));
+qONH = readtable('nyu onh matched.xlsx');
+qMacula = readtable('nyu mac matched.xlsx');
+[~,fONH,~] = fileparts(qONH.file_name);
+[~,fMacula,~] = fileparts(qMacula.file_name);
 qlist = [];
 for i = 1 : length(flist)
     
@@ -23,11 +23,10 @@ for i = 1 : length(flist)
         continue
     end
     qs = lower(tidx.qualification_status);
-    if any(strcmp(qs,'no'))
-        continue
-    end
+    if any(strcmp(qs,'yes'))      
         qlist = [qlist,flist(i)];
         src = fullfile(flist(i).folder,fname);
         cmd = ['cp "' src '".* ' target];
         system(cmd);
     end
+end